Hardware / OS / Software
Host: Linux Mint 18 Cinnamon 64-bit (fully updated); Kernel version 4.4.0-47-generic
Guest: Windows 8.1 Pro 64-bit (fully updated)
Processor: Intel Core i7-4700HQ, (6MB cache, 4 physical cores, or 8 using Hyper-Threading), CPU Benchmark
VirtualBox: Version 5.1.10 r112026 (Qt5.5.1)
Guest Additions: Installed and up-to-date
Benchmark Tool #1: WinRAR version 5.40 final 64-bit
Benchmark Tool #2: VeraCrypt version 1.19 final 64-bit
Preparation
In both cases I waited after boot until the CPU, RAM, disk drive are at stable near zero-point hits.
Method
- Cloning the original virtual machine to have two identical ones.
- I have, for the second pass, since the reboot disabled Antivirus pointed out at the bottom of this answer and updated WinRAR in both cases from a Beta to the Final version.
- I have done the same Preparation as pointed out earlier.
- The virtual machine ran in foreground, without any other CPU time hungry application running, I have disabled what I could for the purpose of the test not being influenced.
- To include potential caching inside or outside the system, I ran the same test twice consequently. The benefit being almost none.
Results
WinRAR
4 cores => 7.5 minutes (shorter time is better)

WinRAR with 4 cores enabled, 1.5GiB processed in 7.5 minutes.
8 cores => 4.5 minutes (shorter time is better)

WinRAR with 8 cores enabled, 1.5GiB processed in 4.5 minutes.
VeraCrypt
4 cores => speed 2.6 GiB/s (higher speed is better)

VeraCrypt with 4 cores enabled, HW-accelerated AES (AES-NI) speed 2.6 GiB/s.
8 cores => speed 3.9 GiB/s (higher speed is better)

VeraCrypt with 8 cores enabled, HW-accelerated AES (AES-NI) speed 3.9 GiB/s.
Conclusion
I could run as many tests as necessary. But I figure, if these two, one of which is rather complex compression test, the second being a set of rather complex encryption tests, what would be the point.
Both of the benchmarks show a marked difference. I see no reason to believe, that their results are inaccurate, as I followed a rather rigorous preparation and method, moreover these tests have taken place in RAM to rule out I/O bottleneck. From my standpoint, the warning mentioned in the question may apply to some conditions, but certainly not all of them. Having shared with you these pretty remarkable results, I am certain for you to agree with me, that this warning probably should not be taken so seriously on modern CPUs featuring Hyper-Threading with the latest VirtualBox version. One thing for sure: Don't take me for the word and test it under your own conditions, before you decide to apply this setting permanently.
New benchmark
Host + Guest: Linux Mint 19.2 "Tina" - Cinnamon (64-bit); both with kernel: 5.3.0-24-generic
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Processor: Intel® Core™ i7-7700HQ; 6 MB Cache, up to 3.80 GHz, 4 physical cores, or 8 using Hyper-Threading, CPU Benchmark comparison
VirtualBox: Version 6.1.0 r135406 (Qt5.9.5)
Guest Additions: Installed and up-to-date
Benchmark Tool: VeraCrypt version 1.24 Hotfix1 64-bit final (web page, direct deb download link)
Preparation and Method
Same as previous benchmark.
Results
VeraCrypt AES encryption with 4 cores
⟶ speed 4.8 GiB/s (higher speed is better)

VeraCrypt AES encryption with 8 cores (Hyper-Threading warning issued)
⟶ speed 7.2 GiB/s (higher speed is better)

Conclusion
Wonderful 50% performance increase with Hyper-Threading enabled, but only with the AES sadly, I will have to run some more comprehensive test. Will be back in a few days with results.